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The Zingiberales are a tropical group of monocotyledons that includes bananas, gingers, and their relatives. The phylogenetic relationships among the eight families currently recognized are investigated here by using parsimony and maximum likelihood analyses of four character sets: morphological features (1), and sequence data of the (2) chloroplast rbcL gene, (3) chloroplast atpB gene, and (4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most-parsimonious tree. None of the molecular datasets alone completely resolves interfamilial relationships. The analyses of the combined molecular dataset provide more resolution than do those of individual genes, and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggests that the Zingiberales originated in the Early Cretaceous and underwent a rapid radiation in the mid-Cretaceous, by which time most extant family lineages had diverged.

We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence variation, and use it to test a priori hypotheses that net venation and vertebrate-dispersed fleshy fruits should undergo concerted convergence, representing independent but often concurrent adaptations to shaded conditions. Our data demonstrate that net venation arose at least 26 times and was lost eight times over the past 90 million years; fleshy fruits arose at least 21 times and disappeared 11 times. Both traits show a highly significant pattern of concerted convergence ( p!10 K9 ), arising 16 times and disappearing four times in tandem. This phenomenon appears driven by even stronger tendencies for both traits to evolve in shade and be lost in open habitats ( p!10 K13 -10 K29 ). These patterns are among the strongest ever demonstrated for evolutionary convergence in individual traits and the predictability of evolution, and the strongest evidence yet uncovered for concerted convergence. The rate of adaptive shifts per taxon has declined exponentially over the past 90 million years, as expected when large-scale radiations fill adaptive zones.

BackgroundThe Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the “abominable mysteries” of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut.Methodology/Principal FindingsWe present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree.Conclusions/SignificanceThis study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family.

To examine relationships and test previous sectional delimitations within Fuchsia, this study used parsimony and maximum likelihood analyses with nuclear ITS and chloroplast trnL-F and rpl16 sequence data for 37 taxa representing all sections of Fuchsia and four outgroup taxa. Results support previous sectional delimitations, except for F. verrucosa, which is related to a Central American clade rather than to section Fuchsia and is described here as a new section Verrucosa. The basal relationships within Fuchsia are poorly resolved, suggesting an initial rapid diversification of the genus. Among the species sampled, there is strong support for a single South Pacific lineage, a southern South American/southern Brazilian lineage, a tropical Andean lineage, and one or two Central American and Mexican lineages. There is no clear support for an austral origin of the genus, as previously proposed, which is more consistent with Fuchsia's sister group relationship with the boreal Circaea. An ultrametric molecular clock analysis (all minimal dates) places the split between Fuchsia and Circaea at 41 million years ago (mya), with the diversification of the modern-day lineages of Fuchsia beginning at 31 mya. The South Pacific Fuchsia lineage branches off around 30 mya, consistent with fossil records from Australia and New Zealand. The large Andean section Fuchsia began to diversify around 22 mya, preceded by the divergence of the Caribbean F. triphylla at 25 mya. The Brazilian members of section Quelusia separated from the southern Andean F. magellanica around 13 mya, and the ancestor of the Tahitian F. cyrtandroides split off from the New Zealand species of section Skinnera approximately 8 mya.

We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales-Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve-and thus undergo concerted convergence-in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P < I0-9 ) and are each even more strongly associated with shaded habitats (P < I0-10 to I0-23 ); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia.

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Bactridinae include about 150 species of spiny Neotropical palms in five genera that are ecologically important in several vegetation types such as open woodland (Acrocomia), lowland rainforest (Astrocaryum, Bactris), and montane forest (Aiphaness). The subtribe also includes the only exclusively lianescent palm genus in the Neotropics (Desmoncus). We present a fully resolved molecular phylogeny of 41 species of Bactridinae, representing all genera as well as most of the currently ac ‐ cepted infrageneric taxa (subgenera, sections etc.) and recently proposed informal groups. Analyses are based on five plastid DNA regions (matK, trnQ‐rps16, rps16 intron, trnD‐trnT, trnL‐trnF) and three nuclear markers (PRK, RPB2, ITS). A combined dataset was analysed with likelihood and parsimony methods. The results show that all accepted taxa at and above the generic level are monophyletic with high support. Astrocaryum alatum and A. mexicanum, recently segregated into a genus of their own (Hexopetion), form a strongly supported monophyletic group sister to the remaining Astrocaryum species. Desmoncus and Acrocomia are resolved as sister genera, and together they are sister to the remaining Bactridinae. This finding contrasts with that of two previous studies reporting Acrocomia to be sister to the rest of the subtribe. Aiphanes is resolved as sister to Bactris and Astrocaryum. Species‐level relationships recovered within Astrocaryum and Bactris disagree to a large extent with previous morphology‐based infrageneric classifications, suggesting that those characters are homoplasious, particularly within Bactris. A Bayesian dating analysis using the relaxed‐clock model indicates that most genera of Bactridinae diverged during a relatively short period around the Eocene–Oligocene boundary, which might explain the difficulties in resolving the phylogenetic backbone of the group. The mostly Andean genus Aiphanes shows an initial radiation of early lineages in the Oligocene (around 25 Ma ago) corresponding to an early uplift phase of the cordillera. These taxa are nowadays restricted to the mountain forests of Colombia and Ecuador. The main diversification of Andean Aiphanes began in the Miocene (around 11 Ma ago). This study provides the first substantial insight into Bactridinae phylogeny and sets the stage for more comprehensively sampled species‐level studies analysing drivers of diversity of Neotropical palms, speciation patterns, character evolution, or biogeography.